I understand where you're coming from, but for what is primarily geared as a children's TV show, there was only so much Timm could do creatively limited to divulge fully on Batmans psychology dealing with multiple super powered humanoids. Become too attached and too trusting, than he would be incapable of being able to have the contingency plan to stop them if they decided to team up and enslave humanity. The fleshed out result of this is: the Justice Lords story arc, and upcoming for Injustice Gods Among Us. You really want to see this mentality, "Justice League: Doom" I think gives the best defense of Batmans mindset of why the Justice League isn't a good idea.

You also have to consider: At this point in TAS universe, Dick Grayson walked out on him and he was 2nd guessing having a sidekick putting a child in harms way to further his crusade against crime and just before The Cadmus Project nightmare, which in TAS universe resulted in Batmans biggest failure losing Tim Drake as Robin. Did they every specify WHEN that happened in the cannon storyline by the way? The only reference I can recall was in JLU: Epilogue and Batman Beyond: Return of the Joker it's quoted by Terry McGuiness Amanda Waller as "left over Cadmus technology". So did Batman come back to Gotham from the Justice League and that's why Tim was alone on patrol? Does he resent Superman for it as well?